Those dash boards and fitting things into them can sap a guy's energy quickly!
Your Naugahyde seams look good---nice fit there. Will you use some sort of screw head finish washers under them or perhaps those upholstery buttons?
On your side barn door and fitting the floor there: My van is only for work/cargo and it was an advantage to extend the plywood floor over the side foot well. I did have to carefully measure to allow the doors to close properly since I'd added plywood/FRP door trim panels. This gives me a bit more space inside and since I have self-fabricated running boards entry/exit isn't an issue at all. Something to think about.
I've also modified both side doors to accommodate small storage spaces. Not a lot but it does allow storing seldom-used but important tools close at hand and securely stowed.
Good call on fitting the side boxes----your mock up didn't account for the window height but otherwise it looks to be fitting together much as you'd planned.
Nice progress!